lib/SGN/Controller/Interactomics.pm

   1 package SGN::Controller::Interactomics;
   2
   3
   4 =head1 NAME
   5
   6 SGN::Controller::Interactomics - Provides and interface for loading of CytoScape via Web Start with interactomic data.
   7
   8
   9 =cut
  10
  11
  12 use Moose;
  13 use URI::FromHash 'uri';
  14
  15
  16 BEGIN { extends 'Catalyst::Controller'; }
  17
  18
  19 =head2
  20
  21    Loads SGN page for Web Start app.
  22
  23 =cut
  24
  25
  26 sub interactomics :Path("/tools/interactomics") :Args(0) {
  27     my ($self, $c) = @_;
  28
  29     $c->stash->{template} = '/interactomics/index.mas';
  30
  31 }
  32
  33
  34
  35 =head2 create_jnlp
  36
  37   Usage: In an html form, pass it the file (.cys or other cytoscape compatible) location with name "Network" and call this URL with the form action.
  38   Desc : Uses the current URL base and a file passed as a parameter to create the body of a jnlp file for loading CytoScape via Web Start with preloaded data.
  39   Ret  : JNLP file that the user's browser should automatically download and run with Java Web Start.
  40   Args : none
  41   Side Effects: ?
  42
  43 =cut
  44
  45 sub create_jnlp :Path("/tools/interactomics/coffee.jnlp") :Args(0) {
  46     my ($self, $c) = @_;
  47
  48     my $codebase = ($c->req->base)."/CytoScape/";
  49
  50     my $file = $c->req->param("Network");
  51
  52     #Content of jnlp file ultimately downloaded by user
  53     #Change this if and only if the CytoScape build at /static/CytoScape is changed in any way.
  54     #codebase is specified on line 44 of this controller
  55     #file is specified on line 176 of this controller
  56     my $doc =  "<?xml version=\"1.0\" encoding=\"UTF-8\"?>
  57 <jnlp codebase=\"".$codebase."\" href=\"\">
  58   <security>
  59     <all-permissions />
  60   </security>
  61   <information>
  62     <title>Cytoscape Webstart</title>
  63     <vendor>Cytoscape Collaboration</vendor>
  64     <homepage href=\"http://cytoscape.org\" />
  65     <offline-allowed />
  66   </information>
  67   <resources>
  68     <j2se version=\"1.5+\" max-heap-size=\"1024M\" />
  69     <!--All lib jars that cytoscape requires to run should be in this list-->
  70     <jar href=\"cytoscape.jar\" />
  71     <jar href=\"lib/cytoscape-geom-spacial.jar\" />
  72     <jar href=\"lib/freehep-util-2.0.2.jar\" />
  73     <jar href=\"lib/biojava-1.4.jar\" />
  74     <jar href=\"lib/resolver.jar\" />
  75     <jar href=\"lib/cytoscape-graph-dynamic.jar\" />
  76     <jar href=\"lib/colt.jar\" />
  77     <jar href=\"lib/phoebe.jar\" />
  78     <jar href=\"lib/activation.jar\" />
  79     <jar href=\"lib/freehep-export-2.1.1.jar\" />
  80     <jar href=\"lib/tclib.jar\" />
  81     <jar href=\"lib/i4jruntime.jar\" />
  82     <jar href=\"lib/FastInfoset.jar\" />
  83     <jar href=\"lib/jaxws-api.jar\" />
  84     <jar href=\"lib/jaxb-impl.jar\" />
  85     <jar href=\"lib/cytoscape-util-intr.jar\" />
  86     <jar href=\"lib/freehep-graphicsio-svg-2.1.1.jar\" />
  87     <jar href=\"lib/saaj-api.jar\" />
  88     <jar href=\"lib/jaxws-tools.jar\" />
  89     <jar href=\"lib/cytoscape-render-export.jar\" />
  90     <jar href=\"lib/freehep-graphicsio-2.1.1.jar\" />
  91     <jar href=\"lib/piccolo.jar\" />
  92     <jar href=\"lib/itext-2.0.4.jar\" />
  93     <jar href=\"lib/glf.jar\" />
  94     <jar href=\"lib/jdom-1.0.jar\" />
  95     <jar href=\"lib/freehep-io-2.0.2.jar\" />
  96     <jar href=\"lib/jaxws-rt.jar\" />
  97     <jar href=\"lib/freehep-jas-plotter-2.2.jar\" />
  98     <jar href=\"lib/freehep-swing-2.0.3.jar\" />
  99     <jar href=\"lib/jhall.jar\" />
 100     <jar href=\"lib/jaxb-api.jar\" />
 101     <jar href=\"lib/junit.jar\" />
 102     <jar href=\"lib/jsr173_1.0_api.jar\" />
 103     <jar href=\"lib/com-nerius-math-xform.jar\" />
 104     <jar href=\"lib/swing-layout-1.0.1.jar\" />
 105     <jar href=\"lib/giny.jar\" />
 106     <jar href=\"lib/undo.support.jar\" />
 107     <jar href=\"lib/commons-cli-1.x-cytoscape-custom.jar\" />
 108     <jar href=\"lib/freehep-graphicsio-ps-2.1.1.jar\" />
 109     <jar href=\"lib/sjsxp.jar\" />
 110     <jar href=\"lib/http.jar\" />
 111     <jar href=\"lib/cytoscape-cruft-obo.jar\" />
 112     <jar href=\"lib/cytoscape-render-stateful.jar\" />
 113     <jar href=\"lib/cytoscape-render-immed.jar\" />
 114     <jar href=\"lib/stax-ex.jar\" />
 115     <jar href=\"lib/ding.jar\" />
 116     <jar href=\"lib/cytoscape-geom-rtree.jar\" />
 117     <jar href=\"lib/jsr250-api.jar\" />
 118     <jar href=\"lib/swingx-2006_10_27.jar\" />
 119     <jar href=\"lib/cytoscape-graph-fixed.jar\" />
 120     <jar href=\"lib/saaj-impl.jar\" />
 121     <jar href=\"lib/cytoscape-task.jar\" />
 122     <jar href=\"lib/wizard.jar\" />
 123     <jar href=\"lib/fing.jar\" />
 124     <jar href=\"lib/coltginy.jar\" />
 125     <jar href=\"lib/freehep-xml-2.1.1.jar\" />
 126     <jar href=\"lib/l2fprod-common-all.jar\" />
 127     <jar href=\"lib/freehep-graphics2d-2.1.1.jar\" />
 128     <jar href=\"lib/freehep-graphicsio-java-2.1.1.jar\" />
 129     <jar href=\"lib/jnlp.jar\" />
 130     <jar href=\"lib/violinstrings-1.0.2.jar\" />
 131     <jar href=\"lib/concurrent.jar\" />
 132     <jar href=\"lib/streambuffer.jar\" />
 133     <jar href=\"lib/looks-2.1.4.jar\" />
 134     <jar href=\"lib/jsr181-api.jar\" />
 135     <!--These are the plugins you wish to load, edit as necessary.-->
 136     <jar href=\"plugins/biopax.jar\" />
 137     <jar href=\"plugins/cPath.jar\" />
 138     <jar href=\"plugins/yLayouts.jar\" />
 139     <jar href=\"plugins/browser.jar\" />
 140     <jar href=\"plugins/GraphMerge.jar\" />
 141     <jar href=\"plugins/CytoscapeEditor.jar\" />
 142     <jar href=\"plugins/psi_mi.jar\" />
 143     <jar href=\"plugins/filter.jar\" />
 144     <jar href=\"plugins/filters.jar\" />
 145     <jar href=\"plugins/ManualLayout.jar\" />
 146     <jar href=\"plugins/linkout.jar\" />
 147     <jar href=\"plugins/cpath2.jar\" />
 148     <jar href=\"plugins/SBMLReader.jar\" />
 149     <jar href=\"plugins/quick_find.jar\" />
 150     <jar href=\"plugins/TableImport.jar\" />
 151     <jar href=\"plugins/AutomaticLayout.jar\" />
 152   </resources>
 153   <!--This starts-up Cytoscape, specify your plugins to load, and other command line arguments.  Plugins not specified here will not be loaded.-->
 154   <application-desc main-class=\"cytoscape.CyMain\">
 155     <argument>-p</argument>
 156     <argument>org.mskcc.biopax_plugin.plugin.BioPaxPlugIn</argument>
 157     <argument>-p</argument>
 158     <argument>org.cytoscape.coreplugin.cpath.plugin.CPathPlugIn</argument>
 159     <argument>-p</argument>
 160     <argument>yfiles.YFilesLayoutPlugin</argument>
 161     <argument>-p</argument>
 162     <argument>browser.AttributeBrowserPlugin</argument>
 163     <argument>-p</argument>
 164     <argument>GraphMerge.GraphMerge</argument>
 165     <argument>-p</argument>
 166     <argument>cytoscape.editor.CytoscapeEditorPlugin</argument>
 167     <argument>-p</argument>
 168     <argument>org.cytoscape.coreplugin.psi_mi.plugin.PsiMiPlugIn</argument>
 169     <argument>-p</argument>
 170     <argument>filter.cytoscape.CsFilter</argument>
 171     <argument>-p</argument>
 172     <argument>cytoscape.filters.FilterPlugin</argument>
 173     <argument>-p</argument>
 174     <argument>ManualLayout.ManualLayoutPlugin</argument>
 175     <argument>-p</argument>
 176     <argument>linkout.LinkOutPlugin</argument>
 177     <argument>-p</argument>
 178     <argument>org.cytoscape.coreplugin.cpath2.plugin.CPathPlugIn2</argument>
 179     <argument>-p</argument>
 180     <argument>sbmlreader.SBMLReaderPlugin</argument>
 181     <argument>-p</argument>
 182     <argument>csplugins.quickfind.plugin.QuickFindPlugIn</argument>
 183     <argument>-p</argument>
 184     <argument>edu.ucsd.bioeng.coreplugin.tableImport.TableImportPlugin</argument>
 185     <argument>-p</argument>
 186     <argument>csplugins.layout.LayoutPlugin</argument>
 187     <argument>-N</argument>
 188     <argument>".$file."</argument>
 189   </application-desc>
 190 </jnlp>";
 191
 192
 193     $c->res->content_type("application/x-java-jnlp-file");
 194     $c->res->body($doc);
 195
 196
 197 }
 198
 199
 200 1;